either isometric or topdown
theyre almost exactly the same, except top down is less graphically complicated and only requires rotation to represent facing direction.
and not all topdown RTSs look bad 
Isometric isn't that hard to implement, this is how I'd do it:
Program it like a topdown, except add a variable "height", and make it so that "height" is an exact multiple of however many pixels the object would be compared to normal. Make the sprites isometric, but get the approximate shape of what the object would look like in topdown, and use that as the mask. Then, draw the sprite of the object in [variable height] pixels above the location. As long as you never have 2 storeys of the same spot accessible (and this almost never happens, if it does, just make it so its 2 separate rooms), you should be fine.
For mouseclicking, make it check the mouseclicks of the sprite. Maybe just make a second object thats related to the first. I don't know really.
Point is, it isn't
that hard to program, it's just hard
er